Following a tense situation between player, the Villarreal board of directors and manager Manuel Pellegrini, Riquelme accepted a five-month loan back to Boca Juniors from February 2007 until 30 June 2007. He joined Boca for the 2007 Torneo Clausura of the 2007–08 Argentine Primera División season, debuting during the 2007 Torneo Clausura in a 1–1 home draw against Rosario Central on 17 February 2007. He scored his first goal for Boca – in his newest stint – in a 1–1 home draw against Independiente on 9 March 2007. He scored in the 54th minute to level the scores. His first goal of the 2007 Copa Libertadores came in Boca's third group-stage match against Mexico's Toluca on 22 March 2007. Riquelme scored in the 23rd minute, Boca's second goal of the match in an eventual 3–0 home victory. Boca finished in second position of their respective group with ten points, advancing to the knockout stages of the competition.
During the knockout stages of the competition, Boca faced Vélez Sarsfield in the round of 16 fixtures. During the first leg on 2 May 2007, Riquelme scored in the first minute as Boca claimed a 3–0 home victory. Having progressed to the quarter-finals, Boca Juniors faced Paraguayan side Club Libertad. During the second-leg of the quarter-finals, played on 24 May 2007, Riquelme scored Boca's first goal in the 61st minute of the match as they claimed a 2–0 away victory and a 3–1 aggregate result, ensuring progression to the semi-finals. During Boca's second-leg semi-final fixture against Colombia's Cúcuta Deportivo on 7 June 2007, Riquelme scored a 44th-minute free kick, scoring Boca's first goal of their 3–0 home victory. After winning 4–3 on aggregate, Boca advanced to the 2007 Copa Libertadores Final, where they would face Brazilian side Grêmio in June 2007.
In August 2007, it was reported that Boca had given up hope of re-signing Riquelme. A few days later, however, the situation changed, with Boca director Juan Carlos Crespi expressing confidence in the player's return "within 10 days". The negotiations stalled when Villarreal's counteroffered to sell Riquelme only in exchange for €4 million, Rodrigo Palacio and half the rights to either Mauro Boselli or Jonathan Maidana, terms which were rejected by Boca. On 30 August 2007, however, it was announced Riquelme had been signed by Atlético Madrid for a fee of €8 million, though the deal fell through at the last minute, leaving Riquelme a Villarreal player. He was given the number 16 shirt for the 2007–08 season. Then, on 26 November 2007, Riquelme reached an agreement with Villarreal to allow his re-joining Boca Juniors when the next transfer window re-opened, in January 2008.
Boca opted to pay Villarreal US$15 million to purchase Riquelme, while Villarreal would pay Riquelme's salary on behalf of Boca Juniors for remainder of the 2007–08 playing season, which was approximately €3 million. The deal was the most expensive fee paid to an Argentine for its respective player in history. Riquelme subsequently signed a contract lasting from the end of 2007 to 2010. He was unable to participate in the 2007 FIFA Club World Cup as he was not registered by FIFA in time to be able to compete at the tournament.
On 26 June 2007, Riquelme was recalled to the national team by coach Alfio Basile as part of Argentina's 23-man squad for 2007 Copa América. During the early morning after Boca Juniors had claimed the 2007 Copa Libertadores, Riquelme hurriedly returned to Buenos Aires and departed with the Argentina national team to Venezuela for the tournament. On 28 June, Riquelme featured in Argentina's opening group stage match, a 4–1 victory against the United States. On 2 July, Argentina faced Colombia in their second group stage match. Riquelme netted twice, with a header in the 34th minute and then with a free-kick in the 45th minute, as Argentina won the match, 4–2.